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Westerlund K, Oroujeni M, Gestin M, Clinton J, Hani Rosly A, Tano H, Vorobyeva A, Orlova A, Eriksson Karlström A, Tolmachev V. Shorter Peptide Nucleic Acid Probes Improve Affibody-Mediated Peptide Nucleic Acid-Based Pretargeting. ACS Pharmacol Transl Sci 2024; 7:1595-1611. [PMID: 38751640 PMCID: PMC11091976 DOI: 10.1021/acsptsci.4c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024]
Abstract
Affibody-mediated PNA-based pretargeting shows promise for HER2-expressing tumor radiotherapy. In our recent study, a 15-mer ZHER2:342-HP15 affibody-PNA conjugate, in combination with a shorter 9-mer [177Lu]Lu-HP16 effector probe, emerged as the most effective pretargeting strategy. It offered a superior tumor-to-kidney uptake ratio and more efficient tumor targeting compared to longer radiolabeled effector probes containing 12 or 15 complementary PNA bases. To enhance the production efficiency of our pretargeting system, we here introduce even shorter 6-, 7-, and 8-mer secondary probes, designated as HP19, HP21, and HP20, respectively. We also explore the replacement of the original 15-mer Z-HP15 primary probe with shorter 12-mer Z-HP12 and 9-mer Z-HP9 alternatives. This extended panel of shorter PNA-based probes was synthesized using automated microwave-assisted methods and biophysically screened in vitro to identify shorter probe combinations with the most effective binding properties. In a mouse xenograft model, we evaluated the biodistribution of these probes, comparing them to the Z-HP15:[177Lu]Lu-HP16 combination. Tumor-to-kidney ratios at 4 and 144 h postinjection of the secondary probe showed no significant differences among the Z-HP9:[177Lu]Lu-HP16, Z-HP9:[177Lu]Lu-HP20, and the Z-HP15:[177Lu]Lu-HP16 pairs. Importantly, tumor uptake significantly exceeded, by several hundred-fold, that of most normal tissues, with kidney uptake being the critical organ for radiation therapy. This suggests that using a shorter 9-mer primary probe, Z-HP9, in combination with 9-mer HP16 or 8-mer HP20 secondary probes effectively targets tumors while minimizing the dose-limiting kidney uptake of radionuclide. In conclusion, the Z-HP9:HP16 and Z-HP9:HP20 probe combinations offer good prospects for both cost-effective production and efficient in vivo pretargeting of HER2-expressing tumors.
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Affiliation(s)
- Kristina Westerlund
- Department
of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology
and Health, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Maryam Oroujeni
- Department
of Immunology, Genetics and
Pathology, Uppsala University, Uppsala 751 23, Sweden
- Affibody
AB, Solna 171
65, Sweden
| | - Maxime Gestin
- Department
of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology
and Health, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Jacob Clinton
- Department
of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology
and Health, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Alia Hani Rosly
- Department
of Immunology, Genetics and
Pathology, Uppsala University, Uppsala 751 23, Sweden
| | - Hanna Tano
- Department
of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology
and Health, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Anzhelika Vorobyeva
- Department
of Immunology, Genetics and
Pathology, Uppsala University, Uppsala 751 23, Sweden
| | - Anna Orlova
- Department
of Medicinal Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Amelie Eriksson Karlström
- Department
of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology
and Health, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Vladimir Tolmachev
- Department
of Immunology, Genetics and
Pathology, Uppsala University, Uppsala 751 23, Sweden
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Li C, Callahan AJ, Phadke KS, Bellaire B, Farquhar CE, Zhang G, Schissel CK, Mijalis AJ, Hartrampf N, Loas A, Verhoeven DE, Pentelute BL. Automated Flow Synthesis of Peptide-PNA Conjugates. ACS CENTRAL SCIENCE 2022; 8:205-213. [PMID: 35233452 PMCID: PMC8874765 DOI: 10.1021/acscentsci.1c01019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/04/2023]
Abstract
Antisense peptide nucleic acids (PNAs) have yet to translate to the clinic because of poor cellular uptake, limited solubility, and rapid elimination. Cell-penetrating peptides (CPPs) covalently attached to PNAs may facilitate clinical development by improving uptake into cells. We report an efficient technology that utilizes a fully automated fast-flow instrument to manufacture CPP-conjugated PNAs (PPNAs) in a single shot. The machine is rapid, with each amide bond being formed in 10 s. Anti-IVS2-654 PPNA synthesized with this instrument presented threefold activity compared to transfected PNA in a splice-correction assay. We demonstrated the utility of this approach by chemically synthesizing eight anti-SARS-CoV-2 PPNAs in 1 day. A PPNA targeting the 5' untranslated region of SARS-CoV-2 genomic RNA reduced the viral titer by over 95% in a live virus infection assay (IC50 = 0.8 μM). Our technology can deliver PPNA candidates to further investigate their potential as antiviral agents.
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Affiliation(s)
- Chengxi Li
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alex J. Callahan
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kruttika S. Phadke
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Bryan Bellaire
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Charlotte E. Farquhar
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Genwei Zhang
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carly K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander J. Mijalis
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David E. Verhoeven
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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Montazersaheb S, Hejazi MS, Nozad Charoudeh H. Potential of Peptide Nucleic Acids in Future Therapeutic Applications. Adv Pharm Bull 2018; 8:551-563. [PMID: 30607328 PMCID: PMC6311635 DOI: 10.15171/apb.2018.064] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker. Considering the unique properties of PNA, including resistance to enzymatic digestion, higher biostability combined with great hybridization affinity toward DNA and RNA, it has attracted great attention toward PNA- based technology as a promising approach for gene alteration. However, an important challenge in utilizing PNA is poor intracellular uptake. Therefore, some strategies have been developed to enhance the delivery of PNA in order to reach cognate site. Although PNAs primarily demonstrated to act as an antisense and antigene agents for inhibition of transcription and translation of target genes, more therapeutic applications such as splicing modulation and gene editing are also used to produce specific genome modifications. Hence, several approaches based on PNAs technology have been designed for these purposes. This review briefly presents the properties and characteristics of PNA as well as different gene modulation mechanisms. Thereafter, current status of successful therapeutic applications of PNA as gene therapeutic intervention in different research areas with special interest in medical application in particular, anti-cancer therapy are discussed. Then it focuses on possible use of PNA as anti-mir agent and PNA-based strategies against clinically important bacteria.
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Affiliation(s)
- Soheila Montazersaheb
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Flory JD, Johnson T, Simmons CR, Lin S, Ghirlanda G, Fromme P. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. ARTIFICIAL DNA, PNA & XNA 2015; 5:1-8. [PMID: 25760314 DOI: 10.4161/1949095x.2014.992181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled PNA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50°C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.
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Key Words
- DBCO, dibenzocyclooctyl
- DNA nanotechnology
- DTNB, 5, 5′-dithiobis-(2-nitrobenzoic acid)
- EtBr, ethidium bromide
- IEX-FPLC, ion-exchange fast protein liquid chromatography
- MALDI-MS, matrix assisted laser desorption ionization mass spectrometry
- PAGE, polyacrylamide gel electrophoresis
- PNA, peptide nucleic acid
- RP-HPLC, reverse-phase high pressure liquid chromatography
- TCEP, tris(2-carboxyethyl)phosphine
- biomimicry
- copper-free click chemistry
- fluorescence
- self-assembly
- γ-PNA
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Affiliation(s)
- Justin D Flory
- a Department of Chemistry and Biochemistry; Arizona State University ; Tempe , Arizona USA
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Ishizuka T, Xu Y, Komiyama M. Clipping of Telomere from Human Chromosomes Using a Chemistry-Based Artificial Restriction DNA Cutter. ACTA ACUST UNITED AC 2015; 61:6.13.1-6.13.13. [PMID: 26344230 DOI: 10.1002/0471142700.nc0613s61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The detection of individual telomere lengths of human chromosomes can provide crucial information on genome stability, cancer, and telomere-related diseases. However, current methods to measure telomere length entail shortcomings that have limited their use. Recently, we have developed a method for detection of individual telomere lengths (DITL) that uses a chemistry-based DNA-cutting approach. The most beneficial feature of the DITL approach is to cleave the sequence adjacent to the telomere followed by resolution of the telomere length at the nucleotide level of a single chromosome. In this unit, a protocol for successful detection of individual telomere lengths from individual chromosomes is described in detail.
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Affiliation(s)
- Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
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Feagin TA, Shah NI, Heemstra JM. Convenient and scalable synthesis of fmoc-protected Peptide nucleic Acid backbone. J Nucleic Acids 2012; 2012:354549. [PMID: 22848796 PMCID: PMC3400375 DOI: 10.1155/2012/354549] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/11/2012] [Indexed: 11/17/2022] Open
Abstract
The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA.
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Affiliation(s)
- Trevor A. Feagin
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Nirmal I. Shah
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
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Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KGC, Enright AJ, Gait MJ, Vigorito E. Efficient inhibition of miR-155 function in vivo by peptide nucleic acids. Nucleic Acids Res 2010; 38:4466-75. [PMID: 20223773 PMCID: PMC2910044 DOI: 10.1093/nar/gkq160] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/24/2010] [Accepted: 02/24/2010] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in diverse physiological processes and are potential therapeutic agents. Synthetic oligonucleotides (ONs) of different chemistries have proven successful for blocking miRNA expression. However, their specificity and efficiency have not been fully evaluated. Here, we show that peptide nucleic acids (PNAs) efficiently block a key inducible miRNA expressed in the haematopoietic system, miR-155, in cultured B cells as well as in mice. Remarkably, miR-155 inhibition by PNA in primary B cells was achieved in the absence of any transfection agent. In mice, the high efficiency of the treatment was demonstrated by a strong overlap in global gene expression between B cells isolated from anti-miR-155 PNA-treated and miR-155-deficient mice. Interestingly, PNA also induced additional changes in gene expression. Our analysis provides a useful platform to aid the design of efficient and specific anti-miRNA ONs for in vivo use.
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Affiliation(s)
- Martin M. Fabani
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Cei Abreu-Goodger
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Donna Williams
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Paul A. Lyons
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Adrian G. Torres
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kenneth G. C. Smith
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anton J. Enright
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J. Gait
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Elena Vigorito
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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